The Treaty of Amiens of 25 March 1802 suspended the activity of the flotilla, but it was reactivated at the outbreak of the War of the Third Coalition in May 1803. Bonaparte reorganised the flotilla, which was regularly attacked by British forces with little effect ; on a background of constant harassing actions between small French and British ships, the flotilla achieved some limited victories against larger British units, such as the Capture of HMS Minerve on 2 July 1803 off Cherbourg, or the Action of 15 July 1805.

On 3 October 1804, a British force under Lord Keith attempted to destroy the flotilla using 25 fireships, which were repelled.[5] The attempt was renewed on 9 October 1806 using Congreve rockets, and the next days by gunfire, with no effect.[6]